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Update nf-core/modules with latest conda fixes
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‎modules.json‎

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@@ -7,212 +7,212 @@
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"nf-core": {
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"bbmap/bbsplit": {
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"branch": "master",
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"git_sha": "656220a9c5b1a56742d40e080a26ed41bfe65373",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"custom/getchromsizes": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "810e8f2603ec38401d49a4aaed06f6d058745552",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"gffread": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["fastq_align_hisat2"]
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},
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"hisat2/build": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"hisat2/extractsplicesites": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "eca65aa4a5e2e192ac44d6962c8f9260f314ffb8",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_markduplicates_picard"]
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},
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"preseq/lcextrap": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"qualimap/rnaseq": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"rsem/calculateexpression": {
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"branch": "master",
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"git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"rsem/preparereference": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"rseqc/bamstat": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/inferexperiment": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/innerdistance": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/junctionannotation": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/junctionsaturation": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/readdistribution": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/readduplication": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/tin": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_rseqc"]
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},
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"salmon/index": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"salmon/quant": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "71961a0773491b49dd96c197877db3434bfc82c6",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": [
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"bam_dedup_stats_samtools_umitools",
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"bam_markduplicates_picard"
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"bam_dedup_stats_samtools_umitools"
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]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_sort_stats_samtools"]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_stats_samtools"]
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},
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"sortmerna": {
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"branch": "master",
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"git_sha": "b499faebd5d56c82d20389c814e9d4618ad42571",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"star/align": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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"branch": "master",
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"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"stringtie/stringtie": {
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"branch": "master",
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"git_sha": "d0e6f468af1d51ce3ea4ac4fb5e58723eac3938c",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"subread/featurecounts": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"trimgalore": {
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"branch": "master",
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"git_sha": "b51a69e30973c71950225c817ad07a3337d22c40",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"ucsc/bedclip": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"ucsc/bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"umitools/dedup": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["bam_dedup_stats_samtools_umitools"]
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},
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"umitools/extract": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"untar": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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}
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}

‎modules/nf-core/bbmap/bbsplit/main.nf‎

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‎modules/nf-core/cat/fastq/main.nf‎

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‎modules/nf-core/custom/dumpsoftwareversions/main.nf‎

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‎modules/nf-core/custom/getchromsizes/main.nf‎

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‎modules/nf-core/fastqc/main.nf‎

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‎modules/nf-core/gffread/main.nf‎

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‎modules/nf-core/gunzip/main.nf‎

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‎modules/nf-core/hisat2/align/main.nf‎

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‎modules/nf-core/hisat2/build/main.nf‎

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